Starting phenix.real_space_refine (version: dev) on Sat Feb 25 23:07:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d46_30571/02_2023/7d46_30571.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d46_30571/02_2023/7d46_30571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d46_30571/02_2023/7d46_30571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d46_30571/02_2023/7d46_30571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d46_30571/02_2023/7d46_30571.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d46_30571/02_2023/7d46_30571.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B ASP 248": "OD1" <-> "OD2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ASP 156": "OD1" <-> "OD2" Residue "E ASP 161": "OD1" <-> "OD2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F ASP 119": "OD1" <-> "OD2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ASP 156": "OD1" <-> "OD2" Residue "F ASP 161": "OD1" <-> "OD2" Residue "F ARG 166": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F ARG 194": "NH1" <-> "NH2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G GLU 295": "OE1" <-> "OE2" Residue "G TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 417": "NH1" <-> "NH2" Residue "G PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 459": "OD1" <-> "OD2" Residue "G ARG 467": "NH1" <-> "NH2" Residue "G GLU 469": "OE1" <-> "OE2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "H TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "H GLU 295": "OE1" <-> "OE2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H ASP 362": "OD1" <-> "OD2" Residue "H TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 417": "NH1" <-> "NH2" Residue "H ASP 458": "OD1" <-> "OD2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "H GLU 469": "OE1" <-> "OE2" Residue "H ASP 490": "OD1" <-> "OD2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 147": "OD1" <-> "OD2" Residue "I PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 246": "OD1" <-> "OD2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I ASP 271": "OD1" <-> "OD2" Residue "I ARG 299": "NH1" <-> "NH2" Residue "I TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 329": "OD1" <-> "OD2" Residue "I GLU 347": "OE1" <-> "OE2" Residue "I PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 65": "NH1" <-> "NH2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 139": "OD1" <-> "OD2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J ASP 199": "OD1" <-> "OD2" Residue "J ASP 206": "OD1" <-> "OD2" Residue "J ARG 211": "NH1" <-> "NH2" Residue "J PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 236": "OD1" <-> "OD2" Residue "J ASP 262": "OD1" <-> "OD2" Residue "J ARG 269": "NH1" <-> "NH2" Residue "J ASP 270": "OD1" <-> "OD2" Residue "J ARG 299": "NH1" <-> "NH2" Residue "J TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 312": "OD1" <-> "OD2" Residue "J ARG 316": "NH1" <-> "NH2" Residue "J TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 387": "OD1" <-> "OD2" Residue "J TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 421": "OE1" <-> "OE2" Residue "J GLU 445": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26636 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2262 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2249 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2489 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2515 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2445 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 11, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2445 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 11, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3358 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Chain: "J" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3373 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Time building chain proxies: 15.26, per 1000 atoms: 0.57 Number of scatterers: 26636 At special positions: 0 Unit cell: (166.11, 166.11, 160.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 4973 8.00 N 4649 7.00 C 16872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.85 Conformation dependent library (CDL) restraints added in 4.3 seconds 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6594 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 37 sheets defined 39.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.844A pdb=" N GLU A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.607A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 62 through 75 removed outlier: 4.184A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 4.465A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.079A pdb=" N ALA A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.977A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.595A pdb=" N LYS A 234 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.552A pdb=" N VAL A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'B' and resid 2 through 16 removed outlier: 4.468A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'B' and resid 62 through 77 removed outlier: 3.689A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 116 removed outlier: 4.527A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 292 through 305 removed outlier: 3.513A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 removed outlier: 3.670A pdb=" N GLY C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 4.372A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 95 Processing helix chain 'C' and resid 129 through 146 removed outlier: 3.750A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.745A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 300 through 304 removed outlier: 3.939A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.972A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.631A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 71 removed outlier: 4.928A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 96 removed outlier: 3.901A pdb=" N ASN D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 146 Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.068A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.815A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.905A pdb=" N VAL D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.773A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.723A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.869A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 46 removed outlier: 3.930A pdb=" N VAL E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.885A pdb=" N GLU E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.666A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.627A pdb=" N LEU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 removed outlier: 4.071A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 235 Processing helix chain 'E' and resid 277 through 292 removed outlier: 4.291A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 46 removed outlier: 3.849A pdb=" N VAL F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'F' and resid 86 through 94 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'F' and resid 114 through 124 removed outlier: 4.215A pdb=" N TYR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.504A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 277 through 292 removed outlier: 4.265A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.960A pdb=" N SER G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.752A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 222 through 239 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.350A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 284 Processing helix chain 'G' and resid 292 through 311 Processing helix chain 'G' and resid 313 through 324 removed outlier: 3.521A pdb=" N GLN G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 327 No H-bonds generated for 'chain 'G' and resid 325 through 327' Processing helix chain 'G' and resid 339 through 350 Processing helix chain 'G' and resid 369 through 377 Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.500A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 430 removed outlier: 4.576A pdb=" N GLN G 422 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 463 removed outlier: 3.860A pdb=" N LEU G 463 " --> pdb=" O PRO G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 516 removed outlier: 3.741A pdb=" N VAL G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 removed outlier: 3.649A pdb=" N SER H 181 " --> pdb=" O SER H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 239 Processing helix chain 'H' and resid 247 through 267 removed outlier: 5.006A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 284 Processing helix chain 'H' and resid 285 through 287 No H-bonds generated for 'chain 'H' and resid 285 through 287' Processing helix chain 'H' and resid 292 through 311 Processing helix chain 'H' and resid 314 through 324 Processing helix chain 'H' and resid 339 through 351 removed outlier: 4.119A pdb=" N THR H 351 " --> pdb=" O GLN H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 377 Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.847A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 390 through 395' Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 439 through 443 removed outlier: 3.800A pdb=" N PHE H 443 " --> pdb=" O THR H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 463 Processing helix chain 'H' and resid 508 through 512 Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.523A pdb=" N ASP I 62 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 87 Processing helix chain 'I' and resid 98 through 107 Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 161 through 175 removed outlier: 3.799A pdb=" N GLU I 175 " --> pdb=" O ARG I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 removed outlier: 4.051A pdb=" N SER I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 262 Processing helix chain 'I' and resid 268 through 279 removed outlier: 3.642A pdb=" N ASN I 279 " --> pdb=" O GLY I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 314 Processing helix chain 'I' and resid 338 through 342 removed outlier: 3.608A pdb=" N ASN I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 63 removed outlier: 4.394A pdb=" N ASP J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 63' Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.792A pdb=" N LEU J 68 " --> pdb=" O ARG J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.689A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.866A pdb=" N GLU J 175 " --> pdb=" O ARG J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 Processing helix chain 'J' and resid 253 through 262 removed outlier: 3.550A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 322 through 326 Processing helix chain 'J' and resid 338 through 342 removed outlier: 3.528A pdb=" N ASN J 341 " --> pdb=" O SER J 338 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 6.451A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 286 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.787A pdb=" N ASN A 208 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.656A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR B 153 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL B 178 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 152 " --> pdb=" O VAL B 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 4.052A pdb=" N LYS C 231 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 247 through 248 removed outlier: 3.668A pdb=" N ALA C 247 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 314 " --> pdb=" O ALA C 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AA9, first strand: chain 'D' and resid 189 through 193 removed outlier: 5.782A pdb=" N THR D 215 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU D 193 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET D 217 " --> pdb=" O GLU D 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 236 through 239 Processing sheet with id=AB2, first strand: chain 'D' and resid 324 through 326 removed outlier: 3.850A pdb=" N SER D 326 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 329 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 51 through 52 removed outlier: 7.036A pdb=" N VAL E 51 " --> pdb=" O VAL E 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 200 through 207 removed outlier: 3.915A pdb=" N ALA E 202 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU E 131 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 204 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA E 129 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU E 128 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE E 266 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET E 130 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LYS E 268 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET E 132 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 167 through 171 Processing sheet with id=AB6, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.968A pdb=" N VAL E 408 " --> pdb=" O ILE E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 7 through 8 removed outlier: 4.012A pdb=" N SER F 105 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N HIS F 203 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA F 202 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ARG F 133 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU F 204 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AB9, first strand: chain 'F' and resid 167 through 170 removed outlier: 6.377A pdb=" N GLY F 159 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL I 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL I 202 " --> pdb=" O PHE I 215 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE I 215 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA I 204 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG I 211 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE I 287 " --> pdb=" O VAL I 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 179 through 183 Processing sheet with id=AC2, first strand: chain 'F' and resid 402 through 405 Processing sheet with id=AC3, first strand: chain 'G' and resid 385 through 387 removed outlier: 3.550A pdb=" N LEU G 386 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP G 362 " --> pdb=" O LEU G 386 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL G 335 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR G 336 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 499 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 507 " --> pdb=" O VAL G 500 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR G 502 " --> pdb=" O GLY G 505 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 407 through 408 removed outlier: 3.888A pdb=" N VAL G 414 " --> pdb=" O THR G 492 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR G 492 " --> pdb=" O VAL G 414 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 385 through 387 removed outlier: 8.944A pdb=" N LEU H 386 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL H 360 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE H 333 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL H 361 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL H 335 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL H 332 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU H 402 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU H 334 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 407 through 408 removed outlier: 3.735A pdb=" N VAL H 414 " --> pdb=" O THR H 492 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 500 through 502 removed outlier: 3.678A pdb=" N ILE H 507 " --> pdb=" O VAL H 500 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 120 through 122 removed outlier: 3.637A pdb=" N ALA I 45 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL I 151 " --> pdb=" O GLN I 44 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL I 46 " --> pdb=" O VAL I 151 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AD1, first strand: chain 'I' and resid 186 through 187 Processing sheet with id=AD2, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.524A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 91 through 94 removed outlier: 7.518A pdb=" N ALA J 45 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE J 94 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU J 47 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL J 46 " --> pdb=" O VAL J 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AD5, first strand: chain 'J' and resid 179 through 182 removed outlier: 4.471A pdb=" N SER J 179 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N HIS J 288 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N MET J 181 " --> pdb=" O HIS J 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 244 through 246 removed outlier: 3.580A pdb=" N LYS J 186 " --> pdb=" O LEU J 245 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE J 185 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 212 through 214 removed outlier: 6.434A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG J 241 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL J 205 " --> pdb=" O GLU J 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 361 through 362 removed outlier: 6.024A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 373 through 375 removed outlier: 3.540A pdb=" N ASP J 392 " --> pdb=" O ILE J 408 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 395 through 396 removed outlier: 6.707A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 919 hydrogen bonds defined for protein. 2610 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.58 Time building geometry restraints manager: 11.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8897 1.34 - 1.46: 4331 1.46 - 1.58: 13665 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 27109 Sorted by residual: bond pdb=" CA ASP D 219 " pdb=" C ASP D 219 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.34e-02 5.57e+03 1.51e+01 bond pdb=" CA SER D 334 " pdb=" C SER D 334 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.59e-02 3.96e+03 1.37e+01 bond pdb=" CA ALA H 349 " pdb=" C ALA H 349 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" C VAL B 193 " pdb=" N ILE B 194 " ideal model delta sigma weight residual 1.334 1.295 0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" CA ALA A 219 " pdb=" C ALA A 219 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.40e-02 5.10e+03 7.85e+00 ... (remaining 27104 not shown) Histogram of bond angle deviations from ideal: 97.36 - 104.91: 479 104.91 - 112.47: 14562 112.47 - 120.02: 10124 120.02 - 127.58: 11370 127.58 - 135.13: 240 Bond angle restraints: 36775 Sorted by residual: angle pdb=" C SER D 326 " pdb=" N ASN D 327 " pdb=" CA ASN D 327 " ideal model delta sigma weight residual 122.65 113.65 9.00 1.66e+00 3.63e-01 2.94e+01 angle pdb=" N ILE A 42 " pdb=" CA ILE A 42 " pdb=" C ILE A 42 " ideal model delta sigma weight residual 113.71 108.63 5.08 9.50e-01 1.11e+00 2.86e+01 angle pdb=" N ASP I 62 " pdb=" CA ASP I 62 " pdb=" C ASP I 62 " ideal model delta sigma weight residual 113.43 107.83 5.60 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N VAL H 488 " pdb=" CA VAL H 488 " pdb=" C VAL H 488 " ideal model delta sigma weight residual 113.20 109.21 3.99 9.60e-01 1.09e+00 1.73e+01 angle pdb=" N VAL J 66 " pdb=" CA VAL J 66 " pdb=" C VAL J 66 " ideal model delta sigma weight residual 112.29 108.57 3.72 9.40e-01 1.13e+00 1.57e+01 ... (remaining 36770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 14333 17.16 - 34.31: 1744 34.31 - 51.47: 348 51.47 - 68.63: 46 68.63 - 85.78: 13 Dihedral angle restraints: 16484 sinusoidal: 6343 harmonic: 10141 Sorted by residual: dihedral pdb=" CA LEU I 431 " pdb=" C LEU I 431 " pdb=" N THR I 432 " pdb=" CA THR I 432 " ideal model delta harmonic sigma weight residual -180.00 -150.90 -29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG H 417 " pdb=" C ARG H 417 " pdb=" N VAL H 418 " pdb=" CA VAL H 418 " ideal model delta harmonic sigma weight residual -180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PHE C 278 " pdb=" C PHE C 278 " pdb=" N PRO C 279 " pdb=" CA PRO C 279 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 16481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2825 0.046 - 0.092: 1153 0.092 - 0.137: 313 0.137 - 0.183: 33 0.183 - 0.229: 3 Chirality restraints: 4327 Sorted by residual: chirality pdb=" CB ILE I 441 " pdb=" CA ILE I 441 " pdb=" CG1 ILE I 441 " pdb=" CG2 ILE I 441 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE J 355 " pdb=" CA ILE J 355 " pdb=" CG1 ILE J 355 " pdb=" CG2 ILE J 355 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO C 279 " pdb=" N PRO C 279 " pdb=" C PRO C 279 " pdb=" CB PRO C 279 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 4324 not shown) Planarity restraints: 4730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO H 396 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO G 396 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 94 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO F 95 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 95 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 95 " 0.030 5.00e-02 4.00e+02 ... (remaining 4727 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 864 2.67 - 3.23: 27854 3.23 - 3.79: 40213 3.79 - 4.34: 51932 4.34 - 4.90: 86508 Nonbonded interactions: 207371 Sorted by model distance: nonbonded pdb=" NZ LYS F 268 " pdb=" O ASN F 271 " model vdw 2.116 2.520 nonbonded pdb=" NH2 ARG C 228 " pdb=" OD2 ASP G 450 " model vdw 2.138 2.520 nonbonded pdb=" O SER D 74 " pdb=" NH2 ARG D 246 " model vdw 2.142 2.520 nonbonded pdb=" O VAL A 63 " pdb=" OG SER A 67 " model vdw 2.155 2.440 nonbonded pdb=" OG SER E 105 " pdb=" OD1 ASP E 107 " model vdw 2.157 2.440 ... (remaining 207366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 253 or resid 268 through 305)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or (resid 122 through 127 and (name N or name \ CA or name C or name O or name CB )) or resid 128 through 351)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 41 through 467) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 16872 2.51 5 N 4649 2.21 5 O 4973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.280 Check model and map are aligned: 0.440 Process input model: 66.490 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.075 27109 Z= 0.515 Angle : 0.930 12.676 36775 Z= 0.539 Chirality : 0.051 0.229 4327 Planarity : 0.005 0.061 4730 Dihedral : 15.192 85.783 9890 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 17.52 % Favored : 82.43 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.12), residues: 3437 helix: -2.23 (0.12), residues: 1212 sheet: -4.58 (0.18), residues: 457 loop : -4.00 (0.12), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 585 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 596 average time/residue: 0.4198 time to fit residues: 387.7674 Evaluate side-chains 416 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 405 time to evaluate : 3.428 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2368 time to fit residues: 9.3601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 0.4980 chunk 260 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 200 optimal weight: 0.0000 chunk 312 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 244 GLN A 270 HIS B 170 HIS C 130 GLN C 158 HIS C 188 HIS C 199 GLN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 154 GLN D 160 HIS D 162 ASN D 242 ASN D 261 HIS D 280 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 271 ASN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 ASN G 275 ASN G 347 GLN G 431 ASN G 478 ASN H 254 ASN ** H 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 ASN I 376 ASN J 44 GLN J 214 HIS J 326 ASN J 352 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 27109 Z= 0.232 Angle : 0.679 11.600 36775 Z= 0.341 Chirality : 0.046 0.253 4327 Planarity : 0.005 0.072 4730 Dihedral : 5.524 26.439 3741 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.13), residues: 3437 helix: -0.71 (0.14), residues: 1219 sheet: -4.08 (0.20), residues: 481 loop : -3.29 (0.13), residues: 1737 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 506 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 42 residues processed: 553 average time/residue: 0.3657 time to fit residues: 328.1923 Evaluate side-chains 460 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 418 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2453 time to fit residues: 23.8071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 259 optimal weight: 0.0010 chunk 212 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 312 optimal weight: 0.9990 chunk 338 optimal weight: 0.9990 chunk 278 optimal weight: 0.8980 chunk 310 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 251 optimal weight: 0.0770 overall best weight: 0.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS D 158 HIS D 162 ASN D 280 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 ASN I 72 ASN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 27109 Z= 0.226 Angle : 0.647 10.911 36775 Z= 0.322 Chirality : 0.045 0.228 4327 Planarity : 0.005 0.076 4730 Dihedral : 5.179 27.389 3741 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.14), residues: 3437 helix: -0.09 (0.15), residues: 1231 sheet: -3.87 (0.19), residues: 504 loop : -2.95 (0.14), residues: 1702 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 460 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 33 residues processed: 519 average time/residue: 0.3595 time to fit residues: 306.2035 Evaluate side-chains 443 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 410 time to evaluate : 3.658 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2471 time to fit residues: 20.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 chunk 210 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 164 optimal weight: 0.0970 chunk 297 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS B 170 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 158 HIS D 154 GLN D 162 ASN D 280 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS H 265 GLN H 274 HIS ** H 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 HIS I 337 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 27109 Z= 0.362 Angle : 0.713 14.563 36775 Z= 0.354 Chirality : 0.047 0.254 4327 Planarity : 0.005 0.072 4730 Dihedral : 5.347 26.642 3741 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.14), residues: 3437 helix: 0.01 (0.15), residues: 1230 sheet: -3.78 (0.20), residues: 461 loop : -2.88 (0.14), residues: 1746 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 425 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 59 residues processed: 490 average time/residue: 0.3676 time to fit residues: 295.9250 Evaluate side-chains 443 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 384 time to evaluate : 3.265 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.2499 time to fit residues: 32.2184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 0.8980 chunk 188 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 247 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS C 199 GLN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 280 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 GLN I 452 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 27109 Z= 0.251 Angle : 0.656 11.727 36775 Z= 0.325 Chirality : 0.046 0.260 4327 Planarity : 0.004 0.079 4730 Dihedral : 5.127 25.614 3741 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.14), residues: 3437 helix: 0.22 (0.15), residues: 1231 sheet: -3.56 (0.20), residues: 501 loop : -2.70 (0.15), residues: 1705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 442 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 40 residues processed: 507 average time/residue: 0.3838 time to fit residues: 322.8074 Evaluate side-chains 424 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 384 time to evaluate : 3.391 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2794 time to fit residues: 25.6992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 0.5980 chunk 299 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 82 optimal weight: 0.0980 chunk 332 optimal weight: 2.9990 chunk 276 optimal weight: 0.0470 chunk 154 optimal weight: 9.9990 chunk 27 optimal weight: 0.0470 chunk 110 optimal weight: 0.9990 chunk 174 optimal weight: 0.0470 overall best weight: 0.1674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 109 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS C 199 GLN D 154 GLN D 162 ASN D 242 ASN D 280 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN H 274 HIS H 347 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 27109 Z= 0.174 Angle : 0.633 14.191 36775 Z= 0.309 Chirality : 0.044 0.260 4327 Planarity : 0.004 0.072 4730 Dihedral : 4.739 24.838 3741 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 3437 helix: 0.57 (0.15), residues: 1225 sheet: -3.24 (0.21), residues: 494 loop : -2.45 (0.15), residues: 1718 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 455 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 20 residues processed: 492 average time/residue: 0.3558 time to fit residues: 286.8931 Evaluate side-chains 420 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 400 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2484 time to fit residues: 13.8610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 0.0970 chunk 37 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 243 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 280 optimal weight: 0.3980 chunk 185 optimal weight: 30.0000 chunk 331 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 153 optimal weight: 30.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS D 162 ASN D 280 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 271 ASN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 27109 Z= 0.247 Angle : 0.663 13.189 36775 Z= 0.321 Chirality : 0.045 0.277 4327 Planarity : 0.004 0.069 4730 Dihedral : 4.766 24.817 3741 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 3437 helix: 0.59 (0.15), residues: 1227 sheet: -3.14 (0.20), residues: 541 loop : -2.43 (0.15), residues: 1669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 407 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 21 residues processed: 441 average time/residue: 0.3622 time to fit residues: 260.4709 Evaluate side-chains 407 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 386 time to evaluate : 3.479 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2503 time to fit residues: 14.3462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 0.5980 chunk 132 optimal weight: 0.1980 chunk 198 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 210 optimal weight: 0.3980 chunk 225 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 260 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS D 154 GLN F 271 ASN F 274 ASN G 213 GLN G 406 HIS ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 27109 Z= 0.208 Angle : 0.648 13.007 36775 Z= 0.313 Chirality : 0.045 0.294 4327 Planarity : 0.004 0.066 4730 Dihedral : 4.683 24.505 3741 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.15), residues: 3437 helix: 0.72 (0.15), residues: 1226 sheet: -2.92 (0.22), residues: 476 loop : -2.30 (0.15), residues: 1735 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 402 time to evaluate : 3.373 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 427 average time/residue: 0.3610 time to fit residues: 253.0591 Evaluate side-chains 403 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 381 time to evaluate : 3.231 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2684 time to fit residues: 15.8411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 3.9990 chunk 317 optimal weight: 0.8980 chunk 289 optimal weight: 6.9990 chunk 308 optimal weight: 0.8980 chunk 185 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 279 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 chunk 307 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS C 280 ASN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 27109 Z= 0.247 Angle : 0.664 15.564 36775 Z= 0.323 Chirality : 0.045 0.310 4327 Planarity : 0.004 0.064 4730 Dihedral : 4.733 24.747 3741 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.15), residues: 3437 helix: 0.71 (0.15), residues: 1227 sheet: -3.00 (0.20), residues: 562 loop : -2.23 (0.15), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 401 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 413 average time/residue: 0.3843 time to fit residues: 260.6626 Evaluate side-chains 389 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 379 time to evaluate : 3.960 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3279 time to fit residues: 11.7368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 4.9990 chunk 326 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 227 optimal weight: 0.0030 chunk 342 optimal weight: 4.9990 chunk 315 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 210 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS D 154 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 27109 Z= 0.228 Angle : 0.662 14.666 36775 Z= 0.322 Chirality : 0.045 0.315 4327 Planarity : 0.004 0.065 4730 Dihedral : 4.695 24.578 3741 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 3437 helix: 0.78 (0.15), residues: 1225 sheet: -2.85 (0.23), residues: 466 loop : -2.19 (0.15), residues: 1746 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 404 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 409 average time/residue: 0.3726 time to fit residues: 249.4382 Evaluate side-chains 389 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 381 time to evaluate : 3.525 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2631 time to fit residues: 8.4689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 1.9990 chunk 290 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123538 restraints weight = 40141.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122439 restraints weight = 56733.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123526 restraints weight = 50271.363| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 27109 Z= 0.280 Angle : 0.691 14.742 36775 Z= 0.338 Chirality : 0.046 0.318 4327 Planarity : 0.005 0.065 4730 Dihedral : 4.803 25.090 3741 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 3437 helix: 0.73 (0.15), residues: 1219 sheet: -2.96 (0.21), residues: 537 loop : -2.19 (0.15), residues: 1681 =============================================================================== Job complete usr+sys time: 5686.51 seconds wall clock time: 104 minutes 43.74 seconds (6283.74 seconds total)